On Thu, 2014-04-24 at 22:05 +0800, Nitin Sharma wrote:
> Dear amber users,
>
> I have been preparing files for MD with following protocol and then later calculating MM/GBSA. I have been doing that with lot of files BUT recently I encountered error in two files while calculating binding free energy. Can you tell me what is wrong
>
> # Ligand preparation using antechamber
> antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc {charge of the ligand}
> parmchk -i ligand.mol2 -f mol2 -o ligand.frcmod
>
> #leaprc
> source leaprc.ff12SB
> source leaprc.gaff
> loadamberparams frcmod.ionsjc_tip3p
> UNK = loadmol2 ligand.mol2
> loadamberparams ligand.frcmod
> saveoff UNK ligand.lib
> saveamberparm UNK ligand.prmtop ligand.inpcrd
> receptor = loadpdb protein.pdb
> saveamberparm receptor receptor.prmtop receptor.inpcrd
> savepdb receptor receptor.pdb
> saveoff receptor receptor.lib
> comp = combine {receptor UNK}
> saveamberparm comp complex.prmtop complex.inpcrd
> savepdb comp complex.pdb
> saveoff comp complex.lib
> addions comp Na+/Cl- 0
> solvateoct comp TIP3PBOX 12.0
> saveamberparm comp complex_solvated.prmtop complex_solvated.inpcrd
> savepdb comp complex_solvated.pdb
> saveoff comp complex_solvated.lib
> quit
>
> #MM/GBSA
> Input file for running PB and GB
> &general
> startframe=1500, verbose=1,entropy=1,
> /
> &gb
> igb=2, qm_theory = 'PM3', saltcon=0.100
> /
> &decomp
> idecomp=2, dec_verbose= 2
> /
>
> #error
> CalcError: sander failed with prmtop complex.prmtop!
That is not the error -- that's just a message that an error occurred.
The actual error will be printed in one of the temporary mdout files.
Something like _MMPBSA_complex_gb.mdout.0 if you are using only 1
processor.
What is the error message in that file?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 24 2014 - 08:00:02 PDT
